Bioindicators of Aquatic Ecosystem Stress 
Biological indicators have been developed and applied at field sites in the eastern U.S. to assess the effects that environmental stressors such as contaminants have on the health of aquatic organisms. (Environmental Sciences Division at Oak Ridge National Laboratory.)
http://www.esd.ornl.gov/programs/bioindicators/Canada's Aquatic Environments 
Featuring the habitats, animals, and plants of Canada's oceans, rivers, lakes, and wetlands. University of Guelph.
http://www.aquatic.uoguelph.ca/
Potholes and Vernal Pools as Potential Indicator Systems 
A technical article by Tim B. Graham about climate change and ephemeral pool ecosystems, with photographs.
http://geochange.er.usgs.gov/sw/impacts/biology/vernal/
Environment Canada: Aquatic Ecosystems 
Part of the Fresh Water web site.
http://www.ec.gc.ca/water/en/nature/aqua/e_aqua.htm
Biological Markers of Water Pollution 
A review of the literature on the use of enzyme induction in aquatic organisms to measure environmental pollution.
http://www.brighton73.freeserve.co.uk/tomsplace/scientific/msc-thesis/mst-revi.htm
Research Group of Experimental Zooplankton Ecology 
A research group in Finland; studies on zooplankton, cyanobacteria, fish and blue mussels in the Baltic Sea -- staff, projects, publications.
http://haavi.fimr.fi/ezeco/
The BioSub Project 
A scientist tries living underwater in an Australian lake, using a self-sustaining habitat. Includes video feed, photograph gallery and latest news.
http://biosub.com.au/